Ligand profile

MCA

Ligand co-crystallized with a similar protein (Protein Data Bank).

Bound to: KP13_01177 — Malonate decarboxylase subunit beta

Via homolog PDB 1on3 UniProt Q8GBW6 Formula C₂₅H₄₀N₇O₁₉P₃S
Mol. weight 867.61 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
MCA
PDB
1on3
UniProt (similar protein)
Q8GBW6
Target protein
KP13_01177

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 867.61 Da
LogP (Crippen) -1.61
H-bond donors 10
H-bond acceptors 20
TPSA 400.93 Ų
Rotatable bonds 21
Aromatic rings 2 / 3
Heavy atoms 55
Fraction sp³ C 0.64
Formula C₂₅H₄₀N₇O₁₉P₃S

Drug-likeness

Descriptor-based ADME screening flags from SMILES. These are not experimental toxicity results.

Permeability proxy Check

Estimated from TPSA and LogP only: TPSA ≤ 90 Ų and −1 ≤ LogP ≤ 5 are treated as a favorable small-molecule permeability screen.

  • TPSA ≤ 90 Ų 400.9
  • −1 ≤ LogP ≤ 5 -1.61
Lipinski's Rule of Five Fail 3 violations
  • MW ≤ 500 Da 867.6
  • LogP ≤ 5 -1.61
  • H-bond donors ≤ 5 10
  • H-bond acceptors ≤ 10 20
Veber's rules Fail
  • Rotatable bonds ≤ 10 21
  • TPSA ≤ 140 Ų 400.9
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
C[C@H](C(=O)O)C(=O)SCCNC(=O)CCNC(=O)[C@@H](C(C)(C)CO[P@@](=O)(O)O[P@@](=O)(O)OC[C@@H]1[C@H]([C@H]([C@@H](O1)n2cnc3c2ncnc3N)O)OP(=O)(O)O)O
InChI 
InChI=1S/C25H40N7O19P3S/c1-12(23(37)38)24(39)55-7-6-27-14(33)4-5-28-21(36)18(35)25(2,3)9-48-54(45,46)51-53(43,44)47-8-13-17(50-52(40,41)42)16(34)22(49-13)32-11-31-15-19(26)29-10-30-20(15)32/h10-13,16-18,22,34-35H,4-9H2,1-3H3,(H,27,33)(H,28,36)(H,37,38)(H,43,44)(H,45,46)(H2,26,29,30)(H2,40,41,42)/t12-,13-,16-,17-,18+,22-/m1/s1
InChIKey 
MZFOKIKEPGUZEN-AGCMQPJKSA-N

Provenance

Annotation context from LigQ_2, the internal Target step that collects PDB, ChEMBL, and ZINC ligand evidence.

Method
LigQ nearest_k
Source
PDB
Binding sites
PF01039

External resources

Open this ligand in third-party databases and cheminformatics tools.

Other ligands for this protein

Quick navigation to other ligands bound to KP13_01177.

PDB 4

Ligands co-crystallized with this protein (structural evidence).

Ligand PDB entry

ZINC 50

Virtual screening candidates selected by structural similarity to known actives (Tanimoto ≥ 0.5).

Compound Similarity (Tanimoto)